SLC19A2 p.Ile193=
c.579C>T · rs749821754 · VCV1950128
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 10.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,908 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000434%
7/1,614,064 alleles · very rare
exomes 5/1,461,888 · genomes 2/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,727 |
| European (non-Finnish) | 0.000254% | 393,349 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SLC19A2
- Protein
- p.Ile193=
- Coding
- c.579C>T
- MANE Select
- NM_006996
- dbSNP
- rs749821754
- Type
- single nucleotide variant
- Location
- chr1:169477383 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.99 · 2 PDB
- Residue 193
- an α-helix
Similar variants
- SLC19A2 c.1223+1G>A Pathogenic ★★ same type
- SLC19A2 c.807+2T>G Likely pathogenic ★★ same type
- SLC19A2 p.Arg162Ter Pathogenic ★★ same type
- SLC19A2 p.Arg397Ter Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gln233Ter Pathogenic ★★ same type
- SLC19A2 p.Glu66Ter Pathogenic ★★ same type
- SLC19A2 p.Gly105Glu Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gly172Asp Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/slc19a2-p-ile193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown